Helix probability profile

Helix-probability profiles are calculated using the method of Zlmm and Bragg. A 3 x3 statistical weight matrix is formulated ... 

Stability of the Cross-Linked Tropomyosin Dimer Cross-Link Effect on the Cooperatlvity of the Ordering Process and on the Maximum in the Helix Probability Profile" Mattice, W. L. Skolnick, J. Macromolecules 1982, IB, 1088. 

If the pertinent cr and s are available, a helix probability profile, depicting the probability for a helical placement as a function of the position in the chain, can be extracted from Z. 

Figure 2. Helix probability profiles deduced for glucagon in water (dashed line) and in aqueous sodium dodecyl sulfate (solid line). Along the bottom of the Figure is the amino acid sequence of glucagon, using A = Ala, D = Asp, F = Fhe, G = Gly,...

Improved reliability of the computed helix probability profiles must await the determination of a and s for the Arg, His, and Lys residues separately. 

Fig. 11. Helix probability profile for human j8-endorphin (peptide 6, Table 2) in water (o) and in the presence of anionic lipids (e). Note that in the absence of lipids there is no potential for the formation of a C-terminal a-helix. Furthermore, the low probability of a-helix formation for a- and y-endorphin may also be correlated with the range of affinities which these peptides exhibit for different opiate receptors.

Discrepancies between retention properties and either summated hydrophobicity or linear hydropathy parameters are expected to become more significant as the molecular size of the solute increases. A number of algorithms are available to predict the secondary structure of peptides and proteins such as the Chou-Fasman [51] method for predicting a-heUx and j8-sheet formation and other procedures [52,53] which determine the probability of heUx formation in a particular solvent environment. These approaches assist in the location of potential hydrophobic areas on the surface of a molecule via characterisation of amphipathic regions. For example, the probability profile shown in Fig. 11 indicates that an amphipathic a-helix can form in the C-terminal region of human )8-endorphin, a peptide which... 

---